Workflow: qiime2 create phylogenetic tree

Fetched 2022-01-20 06:54:23 GMT

Generate a tree for phylogenetic diversity analyses from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

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Inputs

ID Type Title Doc
representative_sequences File
masked_aligned_rep_seqs_filename String
unrooted_tree_filename String
rooted_tree_filename String
aligned_rep_seqs_filename String

Steps

ID Runs Label Doc
create_tree_from_alignment
../tools/qiime2/phylogeny-fasttree.cwl (CommandLineTool)
qiime2: Construct a phylogenetic tree with FastTree
align_representative_sequences
../tools/qiime2/alignment-mafft.cwl (CommandLineTool)
qiime2: Perform de novo multiple sequence alignment using MAFFT
mask_representative_sequences
../tools/qiime2/alignment-mask.cwl (CommandLineTool)
qiime2: Mask unconserved and highly gapped columns from an alignment
root_tree
../tools/qiime2/phylogeny-midpoint-root.cwl (CommandLineTool)
qiime2: Midpoint root an unrooted phylogenetic tree

Outputs

ID Type Label Doc
rooted_tree File
aligned_representative_sequences File
unrooted_tree File
masked_representative_sequences File
Permalink: https://w3id.org/cwl/view/git/a6a7d5bd034f8ccf01b809bc9f5ecf87e5c5652c/subworkflows/qiime2-05-phylogeny.cwl